TABLE 3.
Crystallization conditions, data collection, and refinement statistics
ASU indicates asymmetric unit.
| BaIMPDHΔS | BaIMPDHΔL·IMP·1 | BaIMPDHΔL·IMP·2 | BaIMPDHΔL·IMP·3 | BaIMPDHΔL·IMP·5 | BaIMPDHΔL·IMP·6 | |
|---|---|---|---|---|---|---|
| Data collection | ||||||
| Space group | P1 | P4 | P1 | P21 | P1 | P1 |
| Cell dimensions | ||||||
| a, b, c (Å) | 84.33, 84.25, 84.31 | 110.85, 110.85, 56.26 | 84.93, 89.88, 104.62 | 83.13, 101.33, 87.27 | 85.37, 89.82, 104.50 | 83.22, 89.39, 103.99 |
| α, β, γ (°) | 110.01, 109.22, 109.19 | 90.00, 90.00, 90.00 | 98.70, 90.32, 96.46 | 90.00, 109.57, 90.00 | 81.41, 90.42, 83.50 | 81.30, 89.95, 83.59 |
| Protein molecules/ASU | 4 | 2 | 8 | 4 | 8 | 8 |
| Wavelength (Å) | 0.9792 | 0.9792 | 0.9792 | 0.9793 | 0.9792 | 0.9793 |
| Resolution (Å)a | 2.25 (2.25-2.24) | 1.90 (1.90-1.93) | 2.60 (2.60-2.64) | 2.80 (2.80-2.85) | 2.70 (2.70-2.75) | 2.60 (2.60-2.64) |
| Unique reflections | 79311 (4081) | 53,268 (2224) | 91,462(4515) | 33,129 (1545) | 82,135 (4094) | 88,256 (4394) |
| Rmerge b | 0.052 (0.469) | 0.090 (0.463) | 0.081(0.407) | 0.154 (0.749) | 0.125 (0.584) | 0.090 (0.426) |
| 〈I/σI〉 | 12.7 (2.7) | 7.5 (1.7) | 11.1(2.2) | 7.4 (1.6) | 6.4 (1.9) | 8.4 (2.2) |
| Completeness (%) | 94.5 (96.2) | 98.3 (81.6) | 98.1(97.1) | 98.4 (93.5) | 98.4 (98.0) | 97.8 (97.8) |
| Redundancy | 2.2 (2.1) | 4.3 (2.0) | 1.9 (1.9) | 3.6 (3.1) | 2.3 (2.0) | 2.2 (2.2) |
| Refinement | ||||||
| Resolution (Å) | 2.25 (2.25-2.29) | 1.90 (1.90-1.93) | 2.60(2.60-2.62) | 2.80 (2.80-2.88) | 2.70 (2.70-2.73) | 2.60 (2.60-2.63) |
| Reflections: work/test set | 75225/4055 | 50,550/2697 | 86,761/4583 | 31,341/1681 | 77,888/4096 | 83,785/4415 |
| Rwork/Rfreec | 0.206 (0.232) | 0.147 (0.184) | 0.170 (0.216) | 0.184 (0.248) | 0.218 (0.260) | 0.194 (0.253) |
| No. of atoms: protein/ligandsd | ||||||
| Water | 9632/32/464 | 5119/116/491 | 20473/479/310 | 9854/208/17 | 20811/526/403 | 20517/376/117 |
| Average B factor (Å2): protein/ligand(s) water | 49.5/50.8/41.0 | 23.4/23.6/30.9 | 45.5/46.9/33.6 | 68.9/65.4/54.7 | 47.3/46.9/34.8 | 60.7/55.5/48.6 |
| Bond lengths (Å) | 0.004 | 0.007 | 0.003 | 0.011 | 0.002 | 0.002 |
| Bond angles (°) | 0.854 | 1.216 | 0.740 | 1.397 | 0.659 | 0.649 |
| Most favored | 92.2 | 96.4 | 96.5 | 97.4 | 95.4 | 95.44 |
| Outliers | 0.08 | 0.31 | 0.33 | 0.00 | 0.48 | 0.36 |
| PDB code | 4MJM | 4MYA | 4MY9 | 4QM1 | 4MYX | 4MY1 |
| Crystallization conditions | 0.2 m sodium chloride, 0.1 m sodium cacodylate pH 6.5, 2 m ammonium sulfate, 16 °C | 5% tacsimate, pH 7.0, 0.1 m HEPES pH 7.0, 10% PEG MME 5000, 16 °C | 5% tacsimate, pH 7.0, 0.1 m HEPES, pH 7.0, 10% PEG MME 5000, 16 °C | 0.02 m magnesium chloride, 0.1 m HEPES, pH 7.5, 22%, PAA 5100, 16 °C | 5% tacsimate, pH 7.0, 0.1 m HEPES, pH 7.0. 10% PEG MME, 16 °C | 0.1 m succinic acid, pH 7.0, 15% PEG 3350, 16 °C |
| Cryo-protection solution | 26% sucrose | 25% glycerol | 25% glycerol | 15% glycerol | 20% ethylene glycol | 20% glycerol |
a Values in parentheses correspond to the highest resolution shell.
b Rmerge = ΣhklΣi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣi|〈Ii(hkl)〉 , where Ii(hkl) is the intensity for the ith measurement of an equivalent reflection with indices h, k, and l.
c R = Σhkl‖Fobs| − |Fcalc‖/Σhkl|Fobs|, where Fobs and Fcalc are observed and calculated structure factors, respectively. Rfree is calculated analogously for the test reflections, which were randomly selected and excluded from the refinement.
d Ligands include all atoms, excluding protein and water atoms.